Bommer started his coaching career with the reserve team of Eintracht Frankfurt between July 1994 and August 1995.[3] After stops at VfR Mannheim where he was head coach between July 1997 and April 1998.[4] Bommer then moved on to Viktoria Aschaffenburg where he was head coach from July 1998 to June 2000.[5] Bommer became head coach Wacker Burghausen in October 2000[3] and won his debut 4–3 against his former club VfR Mannheim.[6] Bommer left and became head coach of 1860 München in July 2004.[3] His tenure ended in December 2004; winning five of his 15 league matches in charge.[3] Bommer's next job was as head coach of 1. FC Saarbrücken.[3] He was there between August 2005 and May 2006.[3] Bommer then went to MSV Duisburg between July 2006 and November 2008; finishing with a league record of 28 wins, 21 draws, and 31 losses.[3] Bommer returned to Wacker Burghausen in July 2011 ans was there until December 2011.[3] He then joined Energie Cottbus the next month and was there until November 2013.[3]